We touched on introns and exons in my bio class, but unfortunately we didn't really talk about why Eukaryotes have introns. It would seem they would have to have some purpose since prokaryotes do not have them and they evolved first chronologically, but I could easily be wrong. Did the junk sections of DNA just evolve there by some sort of randomness or necessity as opposed to an actual evolutionary advantage? Why hasn't evolution stopped us from having introns since they seem to be a 'waste' of time and DNA? Why do prokaryotes not have introns?

Not everything needs a function to exist in biology. One way to answer this question is to look to see what kind of selection pressure is acting on introns. Do they evolve neutrally?
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KevinApr 4 '13 at 18:28

3 Answers
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There is still a lot to be learned about the roles introns play in biological processes, but there are a couple of things that have been pretty well established.

Introns enable alternative splicing, which enables a single gene to encode multiple proteins that perform different functions under different conditions. For example, a signal the cell receives could cause an exon that is normally included to be skipped, or an intron that is normally spliced out to be left in for translation (the Wikipedia article on the subject has a basic overview of the possibilities). This would not be possible, or at least would be much more difficult, without the presence of introns.

In recent years, we have discovered that RNA molecules (especially small RNAs such as siRNAs and miRNAs) are much more involved in regulating gene expression than previously thought. Often the small regulatory RNAs are derived from spliced introns.

There is probably more, but essentially introns enable a finer level of regulatory control. Biological complexity is often not the result of having a larger complement of genes, but of having additional layers of regulation to turn genes on and off at the right times. Prokaryotic genes are often organized into operons, and a single polycistronic mRNA will often encode multiple proteins from multiple adjacent genes. Since the biological processes required to sustain microbial life are much less complicated than those required to sustain eukaryotic life, they can get away with much less regulatory control.

I would add that there is a general assumption that this is a reason that eukaryotes might have the ability to adapt to roles higher on the food chain than prokaryotes, like form multicellular organisms (there are a few exceptions, but really very few and they are pretty simple like - cyanobacteria which form chains of cells).
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shigetaApr 8 '12 at 3:56

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While this is a good "how" answer that resumes what we know now, is not by any means a "why" answer. For example, what's the limitation of prokariotic regulation that introns solve? Why do nature needs to squeeze more proteins in a single gene and then have 93% of garbage in the rest of the genome? I think that the answer by @apoz it is a better fit.
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dsignAug 20 '12 at 6:45

I was under the impression that a lot of our introns were just from retroviruses that got into our genome at some point in our evolutionary past. Since the competitive disadvantage incurred by carrying some non-expressed junk DNA is very low, there's not selection pressure to get them back out.
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octernNov 8 '12 at 15:13

Michael Lynch and John Conery (2003) have pointed out that a variety
of genomic features that appear to have little fitness advantage for
organisms-introns, transposable elements, large tracts of noncoding
DNA-may be more prevalent in species with small effective population
sizes. They have suggested that viruses and bacteria have extremely
large population sizes that facilitate the sweep of advantageous
mutations that enable genomic streamlining. By contrast, eukaryotes
have smaller population sizes that facilitate the fixation of
nonadaptive traits. This is the best hypothesis advanced
so far that would explain the diversity of genome sizes and
structures.

I was explaining it to my girlfriend: imagine you have two rooms in your two-and-a-kitchen house full of cartridges of adhesive tape... you really don't need it, but have no way of getting rid of it. Now, the hose of the vacuum cleaner gets broken, and you take a small amount of adhesive tape (you have so much) and patch it... nobody would seriously believe that you were storing all that much adhesive tape for that sake, and you rather should have ordered a new hose. But you did the best of your circumstances. That much is going on in eukariotic genetics: easy and dirty patches everywhere.
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dsignAug 20 '12 at 7:06

I think the Lynch and Conery paper is so far the most reasonable explanation on the origin of introns, and combined with the other answer (biology.stackexchange.com/a/1725/658), it gives a complete explanation about the origin and the current fitness advantage of having introns in certain organisms, but not in others.
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719016Nov 9 '12 at 13:09

Hi apoz - this answer is considered useful by the community but still needs to consist of more than direct quotes.
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Rory M♦Nov 20 '12 at 0:48

@149781-32509185: the Lynch & Conery paper does not explain introns by saying they have a fitness advantage. A small population size that they refer to means that genetic drift is creating the fixation of the introns.
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KevinApr 4 '13 at 18:32

Prokaryotes can't have introns, because they have transcription coupled to translation. They don't have time/space for that, since intron splicing will stop the coupling. Eukaryotes evolved the nucleus, where splicing can be done. The ancestor of eukaryotes that developed the nucleus could afford more variability (because of introns) than species without it, so they had a greater fitness.

Bacteria can't afford high complexity compartmentalization, a process that requires a lot of available energy per gene, a eukaryotic cell can have tens, hundreds or even thousands of mitochondria that have similar energy output to a bacterial cell, while having a genome about 100-500 times smaller (16 kb of a human mitochondria compared to 4.000 kb for a E. coli cell).

I hope that clarifies your doubts, and you can see that this is a debatable answer.

This is a good answer. Comparing the lack of introns between prokaryotes with eukaryotes that do have introns does not mean that introns exist in eukaryotes because it infers an evolutionary advantage to have them. A more likely reason is that introns are highly deleterious in prokaryotes due to genome size limits but not deleterious in eukaryotes. See the C-value problem.
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KevinApr 4 '13 at 18:36